Objective Cigarette smoking exacerbates the progression of pulmonary tuberculosis(TB).The role of tertiary lymphoid structures(TLS)in chronic lung diseases has gained attention;however,it remains unclear whether smoki...Objective Cigarette smoking exacerbates the progression of pulmonary tuberculosis(TB).The role of tertiary lymphoid structures(TLS)in chronic lung diseases has gained attention;however,it remains unclear whether smoking-exacerbated lung damage in TB is associated with TLS.This study aimed to analyze the characteristics of pulmonary TLS in smokers with TB and to explore the possible role of TLS in smoking-related lung injury in TB.Methods Lung tissues from 36 male patients(18 smokers and 18 non-smokers)who underwent surgical resection for pulmonary TB were included in this study.Pathological and immunohistological analyses were conducted to evaluate the quantity of TLS,and chest computed tomography(CT)was used to assess the severity of lung lesions.The correlation between the TLS quantity and TB lesion severity scores was analyzed.The immune cells and chemokines involved in TLS formation were also evaluated and compared between smokers and non-smokers.Results Smoker patients with TB had significantly higher TLS than non-smokers(P<0.001).The TLS quantity in both the lung parenchyma and peribronchial regions correlated with TB lesion severity on chest CT(parenchyma:r=0.5767;peribronchial:r=0.7373;both P<0.001).Immunohistochemical analysis showed increased B cells,T cells,and C-X-C motif chemokine ligand 13(CXCL13)expression in smoker patients with TB(P<0.001).Conclusion Smoker TB patients exhibited increased pulmonary TLS,which was associated with exacerbated lung lesions on chest CT,suggesting that cigarette smoking may exacerbate lung damage by promoting TLS formation.展开更多
Changes in the intestinal immune micro-environment of the gastrointestinal tract are indispensable in the occurrence and development of gastrointestinal cancer.Tertiary lymphoid structure(TLS)is an immune cell aggrega...Changes in the intestinal immune micro-environment of the gastrointestinal tract are indispensable in the occurrence and development of gastrointestinal cancer.Tertiary lymphoid structure(TLS)is an immune cell aggregation structure found around gastrointestinal cancer in recent years.More and more research proves that tertiary lymphoid structure plays a key biological role and clinical value in disease progression,patient prognosis,and adjuvant treatment.This review aims to explore the research progress,biological significance,and potential clinical applications of TLSs in gastrointestinal tumors.The formation,development,and interaction of TLSs with tumor microenvironment have been reviewed and analyzed in recent years.Meanwhile,this review not only evaluates the clinical value of TLSs as prognostic biomarkers and predictors of treatment response but also explores their role in guiding the formulation of immunotherapy strategies for gastrointestinal tumors.In addition,this review points out the main problems in the current research of TLSs and looks forward to their future development,especially their broad application prospects in the diagnosis,treatment,and prognostic evaluation of gastrointestinal tumors.展开更多
This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplif...This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplified model of protein structure. The lowest-energy values required for forming the native conformation of proteins are searched by GATS, and then the coarse structures （i.e., simplified structure） of the proteins are obtained according to the multiple angle parameters corresponding to the lowest energies. All the coarse structures form single hydrophobic cores surrounded by hydrophilic residues, which stay on the right side of the actual characteristic of protein structure. It demonstrates that this approach can predict the 3D protein structure effectively.展开更多
β-TCP, as one of calcium phosphates ceramics, exerts perfect biocompatibility and osteoconductivity, and is clinically used as a bone graft substitute for decades. Consequently, the effects of β-TCP ceramics on intr...β-TCP, as one of calcium phosphates ceramics, exerts perfect biocompatibility and osteoconductivity, and is clinically used as a bone graft substitute for decades. Consequently, the effects of β-TCP ceramics on intracellular Ca2＋ concentration, mineralization of osteoblast and BSA protein structure were studied. Results showed that β-TCP could increase the intracelluar Ca2＋ concentration and mineralization of osteoblast, indicating that β-TCP ceramics could take part in the organic metabolism and the degradation product had no detrimental effect on osteoblast in vitro. Furthermore, β-TCP ceramics could increase the content of α-helix and β-pleated sheet and change BSA into more ordering structure, those changes might be favorable for the biomineralization after β-TCP ceramics implanted.展开更多
In this paper, the applications of evolutionary algorithm in prediction of protein secondary structure and tertiary structures are introduced, and recent studies on solving protein structure prediction problems using ...In this paper, the applications of evolutionary algorithm in prediction of protein secondary structure and tertiary structures are introduced, and recent studies on solving protein structure prediction problems using evolutionary algorithms are reviewed, and the challenges and prospects of EAs applied to protein structure modeling are analyzed and discussed.展开更多
A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physic...A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low energy configurations for a given monomer chain. An ＂off-trap＂ strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13≤n ≤55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55, the algorithm finds new low energy configurations different from those given in literatures.展开更多
The hydrophobic-polar (HP) lattice model is an important simplified model for studying protein folding. In this paper, we present an improved ACO algorithm for the protein structure prediction. In the algorithm, the &...The hydrophobic-polar (HP) lattice model is an important simplified model for studying protein folding. In this paper, we present an improved ACO algorithm for the protein structure prediction. In the algorithm, the "lone"ethod is applied to deal with the infeasible structures, and the "oint mutation and reconstruction"ethod is applied in local search phase. The empirical results show that the presented method is feasible and effective to solve the problem of protein structure prediction, and notable improvements in CPU time are obtained.展开更多
A distance measure that infers to indicate the evolutionary relationship of protein structures has been developed based on spatial preference factors of residues. The spatial preference factor is a reflection of the e...A distance measure that infers to indicate the evolutionary relationship of protein structures has been developed based on spatial preference factors of residues. The spatial preference factor is a reflection of the environment of residues in tertiary structure. Compared with the phyletic relationships derived from sequence homologies and three-dimensional structures, we find that the two lines of evolution are similar in general. This approach is applied to a group of glins here.展开更多
Potassium-ion batteries(KIBs)are a potential candidate to lithium-ion batteries(LIBs)but possess unsatisfactory capacity and rate properties.Herein,the metallic cobalt selenide quantum dots(Co0.85Se-QDs)encapsulated i...Potassium-ion batteries(KIBs)are a potential candidate to lithium-ion batteries(LIBs)but possess unsatisfactory capacity and rate properties.Herein,the metallic cobalt selenide quantum dots(Co0.85Se-QDs)encapsulated in mesoporous carbon matrix were designed via a direct hydrothermal method.Specifically,the cobalt selenide/carbon composite(Co0.85Se-QDs/C)possesses tertiary hierarchical structure,which is the primary quantum dots,the secondary petals flake,and the tertiary hollow micropolyhedron framework.Co0.85Se-QDs are homogenously embedded into the carbon petals flake,which constitute the hollow polyhedral framework.This unique structure can take the advantages of both nanoscale and microscale features:Co0.85Se-QDs can expand in a multidimensional and ductile carbon matrix and reduce the K-intercalation stress in particle dimensions;the micropetals can restrain the agglomeration of active materials and promote the transportation of potassium ion and electron.In addition,the hollow carbon framework buffers volume expansion,maintains the structural integrity,and increases the electronic conductivity.Benefiting from this tertiary hierarchical structure,outstanding K-storage performance(402 mAh g?1 after 100 cycles at 50 mA g?1)is obtained when Co0.85Se-QDs/C is used as KIBs anode.More importantly,the selenization process in this work is newly reported and can be generally extended to prepare other quantum dots encapsulated in edge-limited frameworks for excellent energy storage.展开更多
Tertiary lymphoid structures(TLSs)are ectopic immune cell aggregations that develop in peripheral tissues in response to a wide range of chronic inflammatory conditions,including infection,autoimmune disease,and cance...Tertiary lymphoid structures(TLSs)are ectopic immune cell aggregations that develop in peripheral tissues in response to a wide range of chronic inflammatory conditions,including infection,autoimmune disease,and cancer.In the tumor microenvironment(TME),the structures of TLSs,including B-cell-and T-cell-enriched areas indicate that the TLSs might be the local site during the initiation and maintenance of humoral and cellular immune responses against cancers.Numerous studies have evaluated the expression of TLSs in different cancer patients and their association with prognoses of cancer patients.It was shown that welldeveloped TLSs characterized by mature B cells synthesized tumor specific antibodies,which were considered as specific markers for a good prognosis.However,there are still some immunosuppressive factors existing in the TLSs that may affect anti-tumor responses.These factors include dysfunctional B cells,regulatory T cells,and T follicular regulatory cells.The complexity and heterogeneity of the TLS composition may affect the function and activity of TLSs;it is therefore essential to fully understand the function and influencing factors in TLSs.It has been reported that checkpoint inhibitors and vaccines are currently being developed to reprogram the TME by establishing mature TLSs to improve cancer immunotherapies.In this review,we focused on recent advances in TLSs in human solid tumors,including structural characteristics and classes,antitumor mechanisms,immunosuppressive factors,and TLSbased therapeutic approaches.展开更多
Tumor-associated tertiary lymphoid structures(TLSs)are ectopic lymphoid formations within tumor tissue,with mainly B and T cell populations forming the organic aggregates.The presence of TLSs in tumors has been strong...Tumor-associated tertiary lymphoid structures(TLSs)are ectopic lymphoid formations within tumor tissue,with mainly B and T cell populations forming the organic aggregates.The presence of TLSs in tumors has been strongly associated with patient responsiveness to immunotherapy regimens and improving tumor prognosis.Researchers have been motivated to actively explore TLSs due to their bright clinical application prospects.Various studies have attempted to decipher TLSs regarding their formation mechanism,structural composition,induction generation,predictive markers,and clinical utilization.Meanwhile,the scientific approaches to qualitative and quantitative descriptions are crucial for TLS studies.In terms of detection,hematoxylin and eosin(H&E),multiplex immunohistochemistry(mIHC),multiplex immunofluorescence(mIF),and 12-chemokine gene signature have been the top approved methods.However,no standard methods exist for the quantitative analysis of TLSs,such as absolute TLS count,analysis of TLS constituent cells,structural features,TLS spatial location,density,and maturity.This study reviews the latest research progress on TLS detection and quantification,proposes new directions for TLS assessment,and addresses issues for the quantitative application of TLSs in the clinic.展开更多
Protein powders from Eisenia foetida were prepared using different drying processes and fractionation. Differential scanning calorimetry was used to show that heat denaturation occurred during the drying process above...Protein powders from Eisenia foetida were prepared using different drying processes and fractionation. Differential scanning calorimetry was used to show that heat denaturation occurred during the drying process above 42°C. Protein solubility was also studied. The addition of dissociating reagents allowed concluding that solubility was decreased during oven drying due to thermo denaturation including hydrogen bonds. The volatile compounds of the different powders were extracted by solid phase micro-extraction and identified by mass spectrometry. Volatile compounds were related to lipid oxidation and Maillard reactions occurring during the preparation of the powders. High drying temperatures led to more volatile compounds resulting from Maillard reactions. In the protein powder preparation process, a fractionation step led to a “pulp fraction” and a “juice fraction” of earthworms. The “pulp fraction” contained less odorant volatile compounds resulting from Maillard reactions than the “juice fraction” did.展开更多
This paper proposes a novel discrete differential geometry of n-simplices. It was originally developed for protein structure analysis. Unlike previous works, we consider connection between space-filling n-simplices. U...This paper proposes a novel discrete differential geometry of n-simplices. It was originally developed for protein structure analysis. Unlike previous works, we consider connection between space-filling n-simplices. Using cones of an integer lattice, we introduce tangent bundle-like structure on a collection of n-simplices naturally. We have applied the mathematical framework to analysis of protein structures. In this paper, we propose a simple encoding method which translates the conformation of a protein backbone into a 16-valued sequence.展开更多
In early of 1960s, I was a graduate student studying on tRNA biochemistry. In the course of the research, the magnesium ions stabilized the tertiary structure of tRNA, resulting in its resistance to enzymatic degradat...In early of 1960s, I was a graduate student studying on tRNA biochemistry. In the course of the research, the magnesium ions stabilized the tertiary structure of tRNA, resulting in its resistance to enzymatic degradation was discovered independently. The experiment of deaminated (denatured) tRNA obtained from native tRNA was designed and conducted and further proved the validity of this finding. It was found that magnesium ions could stabilize the tertiary structure of the natrive tRNA but could not stabilize structure of the deaminated tRNA. In term of the methodology, this stabilization technique has been widely applied in sequencing analysis of RNA and has greatly promoted the progress in the study of primary structure of RNA. More importantly, the stabilization of the tertiary structure of RNA by magnesium ions plays a key role both in the processing of messenger RNAs and the ribozyme activity. After our first article in Chinese was published in 1963, a paper of Nishimura & Novelli came into our note. The received date of their paper was March 22 of 1963, only 4 days earlier than that of our first paper. Thus, we and Nishimura & Novelli made almost at the same time the earliest discovery of the role of magnesium ions on stabilizing the tertiary structure of the transfer RNA and thus resulted in resistance of tRNA degradation by enzymes. However, this discovery was not initially appreciated for a period of time but was finally “visualized” and proved by X-ray crystal structure of yeast phenylalanine tRNA, which has provided more accurate information on the geometry of the magnesium-binding sites in tRNA.展开更多
Plant phenolic acids are good sources of antioxidants and sinapic acid(SA)is one of them that can be applied in protein-based food system.However,little research is available regarding interactions between almond prot...Plant phenolic acids are good sources of antioxidants and sinapic acid(SA)is one of them that can be applied in protein-based food system.However,little research is available regarding interactions between almond protein(AP)and SA.In this study,structure-affinity interaction between SA and AP,structure and antioxidant activity of proteins were investigated.Different mathematical models showed that Ka of binding SA and AP were 3.27×10^4 L/mol and 3.08×10^4 L/mol.CD(Circular dichroism)spectroscopy and FT-IR(Fourier transform infrared)spectroscopy showed that the amount of random coil andα-helix decreased whileβ-sheet increased in AP-SA complex.In combination,the interaction model of AP-SA complex was static quenching and attributed to hydrophobic interaction.Further,AP-SA complex exerted better DPPH radical scavenging ability(36.97±0.78%),ABTS+radical scavenging ability(47.26±0.45%),and higher ORAC value(2.41±0.23 M trolox/g)compared to AP.In the further,SA can be applied in protein matrix to improve film stability,gel strength and restraining fat oxidation degradation.展开更多
This work demonstrates the so-called PCAC (Protein principal Component Analysis Clustering) method, which clusters large-scale decoy protein structures in protein structure prediction based on principal component anal...This work demonstrates the so-called PCAC (Protein principal Component Analysis Clustering) method, which clusters large-scale decoy protein structures in protein structure prediction based on principal component analysis (PCA), is an ultra-fast and low-memory-requiring clustering method. It can be two orders of magnitude faster than the commonlyused pairwise rmsd-clustering (pRMSD) when enormous of decoys are involved. Instead of N(N – 1)/2 least-square fitting of rmsd calculations and N2 memory units to store the pairwise rmsd values in pRMSD, PCAC only requires N rmsd calculations and N × P memory storage, where N is the number of structures to be clustered and P is the number of preserved eigenvectors. Furthermore, PCAC based on the covariance Cartesian matrix generates essentially the identical result as that from the reference rmsd-clustering (rRMSD). From a test of 41 protein decoy sets, when the eigenvectors that contribute a total of 90% eigenvalues are preserved, PCAC method reproduces the results of near-native selections from rRMSD.展开更多
HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops-a structural basis for protein domain hierarchy. The server is...HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops-a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural “alphabet” of loops and locks.展开更多
In this paper, a recently proposed dimensional-ity reduction method called Twin Kernel Em-bedding (TKE) [10] is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity mea...In this paper, a recently proposed dimensional-ity reduction method called Twin Kernel Em-bedding (TKE) [10] is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity measures of the input and the embedding spaces expressed by their respective kernels, TKE ensures that both local and global proximity information are preserved simultaneously. Experiments conducted on a subset of the Structural Classification Of Pro-tein (SCOP) database confirmed the effective-ness of TKE in preserving the original relation-ships among protein structures in the lower di-mensional embedding according to their simi-larities. This result is expected to benefit sub-sequent analyses of protein structures and their functions.展开更多
The research methods of protein structure prediction mainly focus on finding effective features of protein sequences and developing suitable machine learning algorithms. But few people consider the importance of weigh...The research methods of protein structure prediction mainly focus on finding effective features of protein sequences and developing suitable machine learning algorithms. But few people consider the importance of weights of features in classification. We propose the GASVM algorithm (classification accuracy of support vector machine is regarded as the fitness value of genetic algorithm) to optimize the coefficients of these 16 features (5 features are proposed first time) in the classification, and further develop a new feature vector. Finally, based on the new feature vector, this paper uses support vector machine and 10-fold cross-validation to classify the protein structure of 3 low similarity datasets (25PDB, 1189, FC699). Experimental results show that the overall classification accuracy of the new method is better than other methods.展开更多
Objective To evaluate the expression of tertiary lymphoid structures (TLS) in renal tissues,and the relationship between TLS and clinicopathological changes and prognosis in idiopathic membranous nephropathy(IMN) pati...Objective To evaluate the expression of tertiary lymphoid structures (TLS) in renal tissues,and the relationship between TLS and clinicopathological changes and prognosis in idiopathic membranous nephropathy(IMN) patients.Methods It was a single center retrospective study.展开更多
基金supported by the Peking University Medicine Fund of Fostering Young Scholars'Scientific&Technological Innovation[grant number BMU2024YFJHPY014]the Fundamental Research Funds for the Central Universities+1 种基金the Key Clinical Projects of Peking University Third Hospital[grant number BYSYZD2022014]the Capital’s Funds for Health Improvement and Research[grant number 2022-2G-40910]。
文摘Objective Cigarette smoking exacerbates the progression of pulmonary tuberculosis(TB).The role of tertiary lymphoid structures(TLS)in chronic lung diseases has gained attention;however,it remains unclear whether smoking-exacerbated lung damage in TB is associated with TLS.This study aimed to analyze the characteristics of pulmonary TLS in smokers with TB and to explore the possible role of TLS in smoking-related lung injury in TB.Methods Lung tissues from 36 male patients(18 smokers and 18 non-smokers)who underwent surgical resection for pulmonary TB were included in this study.Pathological and immunohistological analyses were conducted to evaluate the quantity of TLS,and chest computed tomography(CT)was used to assess the severity of lung lesions.The correlation between the TLS quantity and TB lesion severity scores was analyzed.The immune cells and chemokines involved in TLS formation were also evaluated and compared between smokers and non-smokers.Results Smoker patients with TB had significantly higher TLS than non-smokers(P<0.001).The TLS quantity in both the lung parenchyma and peribronchial regions correlated with TB lesion severity on chest CT(parenchyma:r=0.5767;peribronchial:r=0.7373;both P<0.001).Immunohistochemical analysis showed increased B cells,T cells,and C-X-C motif chemokine ligand 13(CXCL13)expression in smoker patients with TB(P<0.001).Conclusion Smoker TB patients exhibited increased pulmonary TLS,which was associated with exacerbated lung lesions on chest CT,suggesting that cigarette smoking may exacerbate lung damage by promoting TLS formation.
文摘Changes in the intestinal immune micro-environment of the gastrointestinal tract are indispensable in the occurrence and development of gastrointestinal cancer.Tertiary lymphoid structure(TLS)is an immune cell aggregation structure found around gastrointestinal cancer in recent years.More and more research proves that tertiary lymphoid structure plays a key biological role and clinical value in disease progression,patient prognosis,and adjuvant treatment.This review aims to explore the research progress,biological significance,and potential clinical applications of TLSs in gastrointestinal tumors.The formation,development,and interaction of TLSs with tumor microenvironment have been reviewed and analyzed in recent years.Meanwhile,this review not only evaluates the clinical value of TLSs as prognostic biomarkers and predictors of treatment response but also explores their role in guiding the formulation of immunotherapy strategies for gastrointestinal tumors.In addition,this review points out the main problems in the current research of TLSs and looks forward to their future development,especially their broad application prospects in the diagnosis,treatment,and prognostic evaluation of gastrointestinal tumors.
基金Supported by the National Natural Science Foundation of China (60975031)the Scientific Research Foundation for the Returned Overseas Chinese Scholars of Ministry of Education of China, the Open Foundation of State Key Laboratory of Bioelectronics of Southeast University, China, and the Natural Science Foundation of Hubei Province, China (2008CDB344 and 2009CDA034)
文摘This paper describes a case study of 3D protein structure prediction of six sequences from protein data bank （PDB） by genetic algorithm and tabu search （GATS）, where off-lattice AB model is considered as a simplified model of protein structure. The lowest-energy values required for forming the native conformation of proteins are searched by GATS, and then the coarse structures （i.e., simplified structure） of the proteins are obtained according to the multiple angle parameters corresponding to the lowest energies. All the coarse structures form single hydrophobic cores surrounded by hydrophilic residues, which stay on the right side of the actual characteristic of protein structure. It demonstrates that this approach can predict the 3D protein structure effectively.
基金Funded by the Research Fund of Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province (AE201037)the Foundation for Talent Recruitment of Yancheng Institute of Technology (XKR2011007)"973" Chinese National Key Fundamental Research and Development Program (No.G1999064701)
文摘β-TCP, as one of calcium phosphates ceramics, exerts perfect biocompatibility and osteoconductivity, and is clinically used as a bone graft substitute for decades. Consequently, the effects of β-TCP ceramics on intracellular Ca2＋ concentration, mineralization of osteoblast and BSA protein structure were studied. Results showed that β-TCP could increase the intracelluar Ca2＋ concentration and mineralization of osteoblast, indicating that β-TCP ceramics could take part in the organic metabolism and the degradation product had no detrimental effect on osteoblast in vitro. Furthermore, β-TCP ceramics could increase the content of α-helix and β-pleated sheet and change BSA into more ordering structure, those changes might be favorable for the biomineralization after β-TCP ceramics implanted.
基金Supported by the National Natural Science Foundation of China(60133010,70071042,60073043)
文摘In this paper, the applications of evolutionary algorithm in prediction of protein secondary structure and tertiary structures are introduced, and recent studies on solving protein structure prediction problems using evolutionary algorithms are reviewed, and the challenges and prospects of EAs applied to protein structure modeling are analyzed and discussed.
基金The National Natural Science Founda-tion of China (No.10471051) and the National Basic Research Program (973) of China (No.2004CB318000)
文摘A three-dimensional off-lattice protein model with two species of monomers, hydrophobic and hydrophilic, is studied. Enligh- tened by the law of reciprocity among things in the physical world, a heuristic quasi-physical algorithm for protein structure prediction problem is put forward. First, by elaborately simulating the movement of the smooth elastic balls in the physical world, the algorithm finds low energy configurations for a given monomer chain. An ＂off-trap＂ strategy is then proposed to get out of local minima. Experimental results show promising performance. For all chains with lengths 13≤n ≤55, the proposed algorithm finds states with lower energy than the putative ground states reported in literatures. Furthermore, for chain lengths n = 21, 34, and 55, the algorithm finds new low energy configurations different from those given in literatures.
文摘The hydrophobic-polar (HP) lattice model is an important simplified model for studying protein folding. In this paper, we present an improved ACO algorithm for the protein structure prediction. In the algorithm, the "lone"ethod is applied to deal with the infeasible structures, and the "oint mutation and reconstruction"ethod is applied in local search phase. The empirical results show that the presented method is feasible and effective to solve the problem of protein structure prediction, and notable improvements in CPU time are obtained.
文摘A distance measure that infers to indicate the evolutionary relationship of protein structures has been developed based on spatial preference factors of residues. The spatial preference factor is a reflection of the environment of residues in tertiary structure. Compared with the phyletic relationships derived from sequence homologies and three-dimensional structures, we find that the two lines of evolution are similar in general. This approach is applied to a group of glins here.
基金financially supported by Beijing Natural Science Foundation(No.2192034)China Postdoctoral Science Foundation(No.2018M631335)National Key R&D Program of China(No.2018YFB0905600).
文摘Potassium-ion batteries(KIBs)are a potential candidate to lithium-ion batteries(LIBs)but possess unsatisfactory capacity and rate properties.Herein,the metallic cobalt selenide quantum dots(Co0.85Se-QDs)encapsulated in mesoporous carbon matrix were designed via a direct hydrothermal method.Specifically,the cobalt selenide/carbon composite(Co0.85Se-QDs/C)possesses tertiary hierarchical structure,which is the primary quantum dots,the secondary petals flake,and the tertiary hollow micropolyhedron framework.Co0.85Se-QDs are homogenously embedded into the carbon petals flake,which constitute the hollow polyhedral framework.This unique structure can take the advantages of both nanoscale and microscale features:Co0.85Se-QDs can expand in a multidimensional and ductile carbon matrix and reduce the K-intercalation stress in particle dimensions;the micropetals can restrain the agglomeration of active materials and promote the transportation of potassium ion and electron.In addition,the hollow carbon framework buffers volume expansion,maintains the structural integrity,and increases the electronic conductivity.Benefiting from this tertiary hierarchical structure,outstanding K-storage performance(402 mAh g?1 after 100 cycles at 50 mA g?1)is obtained when Co0.85Se-QDs/C is used as KIBs anode.More importantly,the selenization process in this work is newly reported and can be generally extended to prepare other quantum dots encapsulated in edge-limited frameworks for excellent energy storage.
基金This study was supported by grants from the National Key R&D Program of China(Grant No.2018YFC1313400)the National Natural Science Foundation of China(Grant No.U20A20375).
文摘Tertiary lymphoid structures(TLSs)are ectopic immune cell aggregations that develop in peripheral tissues in response to a wide range of chronic inflammatory conditions,including infection,autoimmune disease,and cancer.In the tumor microenvironment(TME),the structures of TLSs,including B-cell-and T-cell-enriched areas indicate that the TLSs might be the local site during the initiation and maintenance of humoral and cellular immune responses against cancers.Numerous studies have evaluated the expression of TLSs in different cancer patients and their association with prognoses of cancer patients.It was shown that welldeveloped TLSs characterized by mature B cells synthesized tumor specific antibodies,which were considered as specific markers for a good prognosis.However,there are still some immunosuppressive factors existing in the TLSs that may affect anti-tumor responses.These factors include dysfunctional B cells,regulatory T cells,and T follicular regulatory cells.The complexity and heterogeneity of the TLS composition may affect the function and activity of TLSs;it is therefore essential to fully understand the function and influencing factors in TLSs.It has been reported that checkpoint inhibitors and vaccines are currently being developed to reprogram the TME by establishing mature TLSs to improve cancer immunotherapies.In this review,we focused on recent advances in TLSs in human solid tumors,including structural characteristics and classes,antitumor mechanisms,immunosuppressive factors,and TLSbased therapeutic approaches.
基金supported by the Key Projects of Sichuan Natural Science Foundation(No.2022NSFSC0051)the Clinical Scientist Program of Sichuan Cancer Hospital(No.YB2022003)the Chengdu Technology Innovation R&D Project(No.2021YF0501659SN),China.
文摘Tumor-associated tertiary lymphoid structures(TLSs)are ectopic lymphoid formations within tumor tissue,with mainly B and T cell populations forming the organic aggregates.The presence of TLSs in tumors has been strongly associated with patient responsiveness to immunotherapy regimens and improving tumor prognosis.Researchers have been motivated to actively explore TLSs due to their bright clinical application prospects.Various studies have attempted to decipher TLSs regarding their formation mechanism,structural composition,induction generation,predictive markers,and clinical utilization.Meanwhile,the scientific approaches to qualitative and quantitative descriptions are crucial for TLS studies.In terms of detection,hematoxylin and eosin(H&E),multiplex immunohistochemistry(mIHC),multiplex immunofluorescence(mIF),and 12-chemokine gene signature have been the top approved methods.However,no standard methods exist for the quantitative analysis of TLSs,such as absolute TLS count,analysis of TLS constituent cells,structural features,TLS spatial location,density,and maturity.This study reviews the latest research progress on TLS detection and quantification,proposes new directions for TLS assessment,and addresses issues for the quantitative application of TLSs in the clinic.
文摘Protein powders from Eisenia foetida were prepared using different drying processes and fractionation. Differential scanning calorimetry was used to show that heat denaturation occurred during the drying process above 42°C. Protein solubility was also studied. The addition of dissociating reagents allowed concluding that solubility was decreased during oven drying due to thermo denaturation including hydrogen bonds. The volatile compounds of the different powders were extracted by solid phase micro-extraction and identified by mass spectrometry. Volatile compounds were related to lipid oxidation and Maillard reactions occurring during the preparation of the powders. High drying temperatures led to more volatile compounds resulting from Maillard reactions. In the protein powder preparation process, a fractionation step led to a “pulp fraction” and a “juice fraction” of earthworms. The “pulp fraction” contained less odorant volatile compounds resulting from Maillard reactions than the “juice fraction” did.
文摘This paper proposes a novel discrete differential geometry of n-simplices. It was originally developed for protein structure analysis. Unlike previous works, we consider connection between space-filling n-simplices. Using cones of an integer lattice, we introduce tangent bundle-like structure on a collection of n-simplices naturally. We have applied the mathematical framework to analysis of protein structures. In this paper, we propose a simple encoding method which translates the conformation of a protein backbone into a 16-valued sequence.
文摘In early of 1960s, I was a graduate student studying on tRNA biochemistry. In the course of the research, the magnesium ions stabilized the tertiary structure of tRNA, resulting in its resistance to enzymatic degradation was discovered independently. The experiment of deaminated (denatured) tRNA obtained from native tRNA was designed and conducted and further proved the validity of this finding. It was found that magnesium ions could stabilize the tertiary structure of the natrive tRNA but could not stabilize structure of the deaminated tRNA. In term of the methodology, this stabilization technique has been widely applied in sequencing analysis of RNA and has greatly promoted the progress in the study of primary structure of RNA. More importantly, the stabilization of the tertiary structure of RNA by magnesium ions plays a key role both in the processing of messenger RNAs and the ribozyme activity. After our first article in Chinese was published in 1963, a paper of Nishimura & Novelli came into our note. The received date of their paper was March 22 of 1963, only 4 days earlier than that of our first paper. Thus, we and Nishimura & Novelli made almost at the same time the earliest discovery of the role of magnesium ions on stabilizing the tertiary structure of the transfer RNA and thus resulted in resistance of tRNA degradation by enzymes. However, this discovery was not initially appreciated for a period of time but was finally “visualized” and proved by X-ray crystal structure of yeast phenylalanine tRNA, which has provided more accurate information on the geometry of the magnesium-binding sites in tRNA.
基金supported by the National Key Research and Development Program of China (2016YFD0401401)The Technological innovation project of Hubei Province (2017ABA142)+2 种基金The Science and Technology Plan Project of Tibet Autonomous Region (XZ201901NA04)The Science and Technology Plan Project of Hunan Science (2017NK2212)The Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2016-OCRI)
文摘Plant phenolic acids are good sources of antioxidants and sinapic acid(SA)is one of them that can be applied in protein-based food system.However,little research is available regarding interactions between almond protein(AP)and SA.In this study,structure-affinity interaction between SA and AP,structure and antioxidant activity of proteins were investigated.Different mathematical models showed that Ka of binding SA and AP were 3.27×10^4 L/mol and 3.08×10^4 L/mol.CD(Circular dichroism)spectroscopy and FT-IR(Fourier transform infrared)spectroscopy showed that the amount of random coil andα-helix decreased whileβ-sheet increased in AP-SA complex.In combination,the interaction model of AP-SA complex was static quenching and attributed to hydrophobic interaction.Further,AP-SA complex exerted better DPPH radical scavenging ability(36.97±0.78%),ABTS+radical scavenging ability(47.26±0.45%),and higher ORAC value(2.41±0.23 M trolox/g)compared to AP.In the further,SA can be applied in protein matrix to improve film stability,gel strength and restraining fat oxidation degradation.
文摘This work demonstrates the so-called PCAC (Protein principal Component Analysis Clustering) method, which clusters large-scale decoy protein structures in protein structure prediction based on principal component analysis (PCA), is an ultra-fast and low-memory-requiring clustering method. It can be two orders of magnitude faster than the commonlyused pairwise rmsd-clustering (pRMSD) when enormous of decoys are involved. Instead of N(N – 1)/2 least-square fitting of rmsd calculations and N2 memory units to store the pairwise rmsd values in pRMSD, PCAC only requires N rmsd calculations and N × P memory storage, where N is the number of structures to be clustered and P is the number of preserved eigenvectors. Furthermore, PCAC based on the covariance Cartesian matrix generates essentially the identical result as that from the reference rmsd-clustering (rRMSD). From a test of 41 protein decoy sets, when the eigenvectors that contribute a total of 90% eigenvalues are preserved, PCAC method reproduces the results of near-native selections from rRMSD.
文摘HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops-a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural “alphabet” of loops and locks.
文摘In this paper, a recently proposed dimensional-ity reduction method called Twin Kernel Em-bedding (TKE) [10] is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity measures of the input and the embedding spaces expressed by their respective kernels, TKE ensures that both local and global proximity information are preserved simultaneously. Experiments conducted on a subset of the Structural Classification Of Pro-tein (SCOP) database confirmed the effective-ness of TKE in preserving the original relation-ships among protein structures in the lower di-mensional embedding according to their simi-larities. This result is expected to benefit sub-sequent analyses of protein structures and their functions.
文摘The research methods of protein structure prediction mainly focus on finding effective features of protein sequences and developing suitable machine learning algorithms. But few people consider the importance of weights of features in classification. We propose the GASVM algorithm (classification accuracy of support vector machine is regarded as the fitness value of genetic algorithm) to optimize the coefficients of these 16 features (5 features are proposed first time) in the classification, and further develop a new feature vector. Finally, based on the new feature vector, this paper uses support vector machine and 10-fold cross-validation to classify the protein structure of 3 low similarity datasets (25PDB, 1189, FC699). Experimental results show that the overall classification accuracy of the new method is better than other methods.
文摘Objective To evaluate the expression of tertiary lymphoid structures (TLS) in renal tissues,and the relationship between TLS and clinicopathological changes and prognosis in idiopathic membranous nephropathy(IMN) patients.Methods It was a single center retrospective study.
